Combatants of the Misunderstood
by KtyouVsWriting
Summary: Commander Jane Shepard was not the only one to have encountered the influence of the Reapers, or was even the first. An Alliance systems engineer known as Isaac Clarke, whose record is kept secret from all but the most important in the Alliance, too, knows of the Reapers. Only the two can understand the true threat. AU, rated M for adult content, language. Paragon, Vanguard.
1. Dossier: Isaac Clarke

Introduction

Classification: **Top-Secret Priority X****  
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Encryption Code: **Classified**

**WARNING - UNAUTHORIZED DISCLOSURE OF FILE CONTENTS PUNISHABLE BY DEATH**

System Alliance Dossier:

First Name: Isaac

Last Name: Clarke

Born: June 5, 2150

Place of Birth: Earth, North America, New York

Mother: Octavia Clarke (Status Unknown)

Father: Poul Clarke (Deceased, Alliance Marine declared KIA)

Graduated: Massachusetts Institution of Technology (summa cum laude)

Degree: Systems Engineering

Affiliations: Human System Alliance

Branch: System Alliance Navy, Alliance Engineering Corp

Rank: Lieutenant

Noteworthy: Interplanetary Combatives Training Graduate (N7)

Participated: Skyllian Blitz, Invasion of Torfan, Battle of the Citadel, Eden Prime War

Isaac Clarke is currently one of the most prominent engineers within all of the System Alliance. As arguably the most prominent student to graduate from Massachusetts Institution of Technology, his understanding of hardware and software technology, from weapons technology to computers to ships has made him one of the most demanded engineers for space battles. He had even begun able to take apart and understand some alien technology, further enhancing his importance. Because of his unique abilities, he was requested aboard numerous ships.

Although he originally enlisted as part of the Systems Alliance to help others as well as to put his engineering skills and talents, it was discovered that some time into his career as an Alliance engineer, he was also a lethal combatant. During his first assignment, Clarke was stationed aboard the dreadnought _SSV Liberator_, a ship that was sent into the enemy territory following the Skyllian Blitz. During the initial assault of one of the moon of Torfan, the _SSC Liberator _sustained heavy damage in the course of the battle, which was followed by Batarian borders. Most of the soldiers assigned to the _Liberator _were slaughtered by the boarding attack. Clarke was ultimately forced to battle through the Batarian boarders in order to secure the the engine room and single-handedly saved the ship from complete destruction. His bravery in the face of insurmountable odds granted him the Medal of Honor.

Clarke's actions also began his training in Interplanetary Combatives Training. He was quick to rise through the ranks, becoming one of the best trainees in the history of the program. In two years, he graduated from ICT and was awarded with the N7 designation. After his graduation, he was immediately given the rank of lieutenant and continued to serve aboard the _SSV Liberator_.

On August 17, 2180, Clarke was part of an expedition that was sent to investigate the mysterious disappearance of the Alliance dreadnought the _SSV Messenger_. Communications between the the _Liberator _and Alliance Command cut out the moment that the _Messenger _was spotted. From that moment, no communications came or went, which put the Admirals on high alert. It was even suggested that another ship be sent, but no ships were sent. Approximately five days after lost communications, a shuttle transmission was received, and Clarke had reported that the mission was a trap set by an enemy of unknown race and with technology beyond our own.

The Lieutenant reviewed mission logs and information data, stating that both the _Liberator _and the _Messenger _were ensnared into a nearby planet designated Arnoxis. The original reason for the _Messenger _being there was due to a massive read of Element Zero, but for some odd reason the ship was somehow rendered inoperable. The crew had been converted into strange animated-like corpses. While Clarke was sent in to try and discern what had become of the crew and what was done to them, the _Liberator_ was attacked and forced closer to the disabled _Messenger_. In the ensuing battle, the _Liberator_ was also disabled and crippled, its crew being turned into these undead creatures.

Despite no backup and no hope of rescue, Clarke, with the help of the skeletal survivors of the _Messenger_, discovered that it was a strange artifact that drew the _Messenger _in to investigate, but the artifact caused the crew to begin to act unusually, slowing becoming something else entirely. Clarke decided that the artifact was too dangerous to be studied and tried to have it destroyed, he was ambushed by the survivors. They took the artifact and began speaking of some ancient race called "Reapers". Any attempts made to dissuade them from their state of mind was met with failure, which prompted Clarke to detonate both the _Liberator _and _Messenger's_ engine cores, effectively destroying both the ships and the mysterious alien artifact.

Clarke was later recovered by an Alliance patrol and was given a full psychiatric examination. Although he was deemed ready to resume active duty, the doctors noted an increase in brain activity. It has been noted that in the previous years, Isaac Clarke has been seen becoming more and more apt in technology, building his own personal suit of armor and weapons, and becoming more and more immersed into engineering in general. However, he remains true to Human System Alliance and to Humanity.

End Dossier

**That Dead Space 3 suit depicting the N7 armor made me think of this. I don't know if this will take off, but I just wanted to get this out. I may not be able to do much with this story as I have a ton of other stories and things going on right now.**

**This gives you a glimpse of the story that this Isaac has been given. It can be open to many interpretations that I have yet to decide on. If I have posted this, I probably already have at least five or more chapters written. With all the things I have to do and the stories to update, keeping up is a lot to do.**

**If you find this story to be worth pursuing, then REVIEW. Tell me what you think about it. Story suggestions and themes can be posted in the review or by PM.**

**Peace!**


	2. Chapter 1: Work is Everything

Chapter 1: Work is Everything

**Jupiter, Sol System**

** Sol System**

** April 9, 2183**

** 06:45 Hours**

_**SSV Titan**_

Isaac Clarke made was quick to move around engineering. His mind was quickly processing everything that he was doing, moving swiftly, but keeping careful note of everything that he was doing. If there was one thing that he didn't like doing, it was being too single-minded. He needed to be aware of his surroundings and keep it all in check. Mistakes were not uncommon, but he wanted to minimize the chances of them occurring.

Isaac Clarke had recently been reassigned to the _SSV_ _Titan_ shortly after a full checkout concerning his story. He didn't really expect everyone to believe his story, which was part of the reason why his armor, at the time, contained video cameras with the log. That time aboard the two overtaken ships was a nightmare, and had he heard himself recounting his own story, he might interpret it as a lunatic's story, but the video logs were proof of what he had discovered, and the Alliance was worried now. An unknown artifact created by an unknown alien that turned them all into mindless slaves with little to no independent thought.

It had been a nightmare the whole time. It was horrible enough slaughtering masses of Alliance personnel that had gone out of their minds. He didn't want to kill them, but he couldn't convince any of them to lay down their weapons, and even when on death's door, nobody wanted to talk, so he had to take matters into his own hands. Going through the ships, he had begun to see a lot of crazy stuff.

He saw some strange writings, a few hallucinations here and there, a few voices when there wasn't' anyone around. It was intimidating, and for once in his life, Isaac was afraid, and it didn't matter if it showed or not. The fear was what drove him to survive, to seek answers fearing not only for his own life but what this could do in the wrong hands. This artifact was too dangerous to use, and dangerous things like this couldn't be controlled by humans or by any other Citadel Council species. Isaac was certain of this, so he destroyed it, but Isaac didn't believe that the threat was over, because it wasn't over.

He knew more about the threat now. The Alliance brass had even contacted him to confirm whether the enemy Isaac faced and the enemy that attacked the Citadel were one in the same, and they were. Apparently, they were called Reapers, and Commander Jane Shepard had faced off against one. It called itself Sovereign, and that its task was to allow its fellow Reapers into the galaxy to continue a process called harvesting. The details were light, but basically, these Reapers sought the destruction of all life, both organic and synthetic.

There was no mistaking it: the Reapers were what he had encountered, or at least their influence. Ever since that incident, he hadn't been the same, so he did the only thing he knew what to do: work harder, keep himself occupied. After facing the nightmares aboard the SSV Liberator, the galaxy was far less scary. He had seen a threat far greater than any race in known space. Commander Shepard as well. The two hadn't even met before, and Isaac, despite having respect for the commander, had no desire to meet her. She was the savior of the galaxy, and she had more important things to care for than a very eccentric engineer.

Isaac had a lot of time to reflect on what he had seen, and he had a greater grasp, but he wanted to know more. His time spent aboard with that strange Reaper artifact might have affected him in more ways than one. Maybe it had tried to take over his mind, tried to control him like it controlled the other occupants of his ship, but maybe it didn't work the way it was intended to. Isaac wasn't stupid when it came to his mental health. He knew better than to dismiss the Reaper's abilities, because they were powerful, something that the galaxy had no idea about. Ironic since he had once been a skeptic about many myths and legends, but after this, he was willing to believe anything because he had seen the face of a true nightmare unlike anything seen before.

Despite his duties aboard the ship, his mind processed things far faster than it use to. He might say that he could even give a Salarian a run for their credits with how fast he could process information. He wasn't sure if it was a good thing or a bad thing that all technology seemed to be simple in his eyes. It had gotten to the point where he had begun to construct his own gear for combat mission should he be called into action. It took some inspiration from the N7 gear that he had received as a complimentary gift from the Alliance after his graduation.

He had made a few modifications, and by a few, he had completely redesigned the software and rewrote the firmware to suit his needs. The armor was bulky, built far more sturdy than it was originally, but he had learned to cope with the extra weight and as a plus, the weight gave him more physical power when in combat.

The suit was also installed with the ability to map through any ship once he had a basic layout of the vessel. All he had to do was to use his suit to guide him should he need the directions, but here on the _Titan_, he didn't need it, as he knew the ship from top to bottom.

His helmet was also a one-of-a-kind helmet, being collapsible. He didn't have to take off his helmet as a separate part; it was now part of this suit and he could summon it on or off in seconds. The helmet was the only part of his armor that wasn't based off the N7, as it was completely designed and integrated himself. It consisted of a visor that would prove to be extreme difficult to hit with a gun.

The most intricate part of Isaac suit was the Element Zero core, which gave him the ability to mimic the abilities of biotics without being a biotic himself. It had taken some hard work and some requisition orders from the Alliance, but he had managed to create an Element Zero core that could simulate biotic abilities. Often, he used biotic lifting abilities in order to move heavy things and because his suit powered these abilities, he could use them in synchronization with his armor systems for fine precision and targeting, making his work easier on large-scale and small-scale construction work. He could also use the eezo to enhance his physical abilities and allow him a short burst of speed. He wanted to make some more upgrades to do as many biotic abilities as he could, but he felt that perhaps they weren't needed now.

The console next to him beeped once and began to display some diagnostics. Turning away from the physical work, the helmet around his head folding away, he focused his attention on the console as it displayed the results of his daily check of the ship's systems. It was probably one of his most nervous and paranoid habits that he had developed after the nightmare operation. The Reapers could take control of Humans, so what's to stop them from taking control of the ship that they were on. There weren't any Reapers here, so he shouldn't worry, and his superiors would be the first to say it, but...they didn't know. Nobody really knew about, except Shepard perhaps, and she was even luckier that she seemingly survived with her sanity intact and her loyalty untouched.

they didn't understand what the Reapers did. The feeling of something in the back of Isaac's mind, it's presence alluring, beguiling, irresistible, things that were scary. Looking back on it, Isaac honestly had no idea what in the galaxy it was, but he did what he thought was best: scream at it, demand it leave, and basically tell it to go to hell, whatever would keep it at bay, things he knew to do, but were they enough? The Alliance brass thought so, otherwise he wouldn't be put back into active duty. He didn't trust himself, even when those around him did.

"Lieutenant," a voice said.

Isaac recognized the voice to be his superior officer, Captain Hammond. He immediately turned around and saluted crisply, his posture not at all lacking.

"Sir," he said, his arms moving behind his back, "I've just completed a routine diagnostics. I'm also prepared to make some core adjustments to increase our output. I've also got some other ideas that requi-"

"Lieutenant," the captain sighed, "Hold your thoughts. Take a breath."

With great reluctance, Isaac did as he was told, but he didn't move himself from his position. He did need to calm down, but he was having a damn hard time doing it with everything on his mind.

"Sorry sir," he said clearly, "Just busy. Shouldn't have bombarded you with the jargon. Just...a lot on my mind."

"I understand," the captain said, "but for God's sake, take a break occasionally. I know that you're an N7 but you work for about twenty hours a day with barely enough sleep."

Isaac tensed for a moment. There was a reason that he didn't sleep, but he didn't tell anyone that. Why should they know anyway? It was likely going to cause a hassle that wasn't necessary. There were far more important things than himself right now.

"Work keeps my mind at ease, sir," Isaac reasoned, "I prefer to spend as much time as possible being productive."

"Isaac," Hammond scolded, "You've been on the _Titan _for less than three years, and you've already done enough work for at least ten years. Engineering can last for a day without you. If you really want to help. the bridge is open. Spend more time with the crew."

"I," Isaac began to object, but he was quick to withdraw.

The other fear he had locked inside was the possibility of himself causing harm to others. Isaac was a firm believer in helping others, and he could recall in the heat of battle a couple of times, trying to help enemy troopers when he could just as easily have executed them. His fight in Torfan with the Batarians, although years ago, felt like it happened yesterday. He didn't see monsters, but simply people who were doing what they thought was right. He couldn't say that he had love for Batarians, but they were living, like himself, so what himself any more special than them?

But as much as Isaac wanted to help others, he wasn't the best social person. Sure, if the topics were interesting, he could easily talk for hours upon hours without pause, but normal discussion about life, about normal things was a little beyond him. He didn't care to talk about his previous life and he didn't have a personal life to speak of. The Alliance was Isaac's life, engineering was his passion, and battle was he was talented at.

"I will...make time for it sir," Isaac answered reluctantly.

Hammond nodded his head and gave him an intense look for a moment before turning to leave, the door closing behind him, the green seal returning to being visible.

Isaac sighed explosively and began to debate if he really should do this. He was the only one in engineering now, but that would change soon. The others would be here. Kyles and Jackson were the top engineer leaders here, and they would no doubt grind him on how hard he was working as well. He wanted to work, he really did. Sure, maybe he did a little excessive fine-tuning, but he did have some legitimate projects that he wanted to work on today, mainly to make some modifications to his plasma cutter. He wanted to get more shots out of a single thermal clip. If his calculations were correct, which they were, he could get about twenty shots, a good amount for its power and weight. He also wanted to experiment with his systems, particularly his Resource Integration Gear, or RIG. He had some ideas on how to use the systems to channel eezo for more effect warp abilities as well as…

_I'm doing it again, _he shook his head. _Maybe I do need a break._

Finally having made up his mind, he reluctantly left a note to the engineers that would come in soon, and took off for the bridge, the Reapers, Torfan, the past forgotten for now…

**My most sincerest apologies for not getting a chapter out sooner, but life has been really busy and other stories have been taking up time.**

**My knowledge of Mass Effect technology is spotty and I'm still learning, but I know enough to know how to work with it.**

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**In the meantime, I hope to have another chapter out by the end of this month.**

**Hope you enjoyed, and remember, take pride in yourself.**

**Peace!**


End file.
